merge Figure 5 into Figure 3

Author: rqthomas

Main_analysis.R

@@ -3,7 +3,7 @@
 #
 library(plotrix)
 
-working_directory <- "/Users/quinn/Dropbox (VTFRS)/Shared_folders/ACONITE/Manuscript 2/2019 ms/analysis/final_rerun_for_reproducability/"
+working_directory <- "/Users/quinn/Dropbox (VTFRS)/Shared_folders/ACONITE/Manuscript 2/2019 ms/analysis/final_rerun_for_reproducability/ACONITE_canopy/"
 figure_directory <- paste(working_directory, "/output/", sep  =  "")
 fortran_code <- "src/aconite_canopy_Rinterface.so"
 ################
@@ -180,15 +180,15 @@ xlab  =  expression(paste("annual respiration (g C ", m^2, " ", yr^-1, ")", sep
 load("output/Rm_at_obs_LAI_TCN_biome3.Rdata")
 ylim  =  range(c(density(par_out_reich[, 2])$y, density(par_out_ryan[,  2])$y),  density(par_out_atkin[,  2])$y)
 xlim  =  c(0,  max(c(density(par_out_reich[, 2])$x, density(par_out_ryan[, 2])$x), density(par_out_atkin[, 2])$x))
-plot(density(par_out_reich[, 2], cut = c(0, 10000)), xlim = xlim, ylim = ylim,  main = "")
-points(density(par_out_atkin[, 2], cut = c(0, 10000)), type = "l", col = "blue")
-points(density(par_out_ryan[, 2], cut = c(0, 10000)), type  =  "l", col = "red")     
+plot(density(par_out_reich[, 2], cut = c(0, 10000)), xlim = xlim, ylim = ylim,  main = "", lty = "dotted")
+points(density(par_out_atkin[, 2], cut = c(0, 10000)), type = "l", col = "blue", lty = "dashed")
+points(density(par_out_ryan[, 2], cut = c(0, 10000)), type  =  "l", col = "red", lty = "solid")     
 mtext("density", side = 2, adj  =  0.6, line  =  2.5, cex = 0.7)
 mtext("Tropical Evergeen", side = 2, adj  =  0.6, line  =  4.5)
 v  =  expression("Canopy R"[leaf][",m"])
 mtext(v, side = 3, adj  =  0.6, line  =  1.0)
 text(xlim[1], ylim[2], "\n   (a)")
-legend("topright", c("Ryan 1991", "Atkin 2016", "Reich 2008"), lty = c(1, 1, 1), col = c("red", "blue", "black"), bty = "n")
+legend("topright", c("Ryan 1991", "Atkin 2016", "Reich 2008"), col = c("red", "blue", "black"), bty = "n", lty = c("solid", "dashed", "dotted"))
 
 #Blank
 plot.new()
@@ -197,9 +197,9 @@ plot.new()
 load("output/Rm_at_obs_LAI_TCN_biome2.Rdata")
 ylim  =  range(c(density(par_out_reich[, 2])$y, density(par_out_ryan[, 2])$y), density(par_out_atkin[, 2])$y)
 xlim  =  c(0, max(c(density(par_out_reich[, 2])$x, density(par_out_ryan[, 2])$x), density(par_out_atkin[, 2])$x))
-plot(density(par_out_reich[, 2], cut = c(0, 10000)), xlim = xlim, ylim = ylim, xlab  =  "annual respiration (gC m-2 yr-1)", ylab  =  "Arctic Evergreen",  main = "")
-points(density(par_out_atkin[, 2], cut = c(0, 10000)), type = "l", col = "blue")
-points(density(par_out_ryan[, 2], cut = c(0, 10000)), type  =  "l", col = "red")        
+plot(density(par_out_reich[, 2], cut = c(0, 10000)), xlim = xlim, ylim = ylim, xlab  =  "annual respiration (gC m-2 yr-1)", ylab  =  "Arctic Evergreen",  main = "", lty = "dotted")
+points(density(par_out_atkin[, 2], cut = c(0, 10000)), type = "l", col = "blue", lty = "dashed")
+points(density(par_out_ryan[, 2], cut = c(0, 10000)), type  =  "l", col = "red", lty = "solid")        
 mtext("density", side = 2, adj  =  0.6, line  =  2.5, cex = 0.7)
 mtext("Arctic Evergreen", side = 2, adj  =  0.6, line  =  4.5)
 text(xlim[1], ylim[2], "\n   (b)")
@@ -210,9 +210,9 @@ plot.new()
 load("output/Rm_at_obs_LAI_TCN_biome1.Rdata")
 ylim  =  range(c(density(par_out_reich[, 2])$y, density(par_out_ryan[, 2])$y), density(par_out_atkin[, 2])$y)
 xlim  =  c(0, max(c(density(par_out_reich[, 2])$x, density(par_out_ryan[, 2])$x), density(par_out_atkin[, 2])$x))
-plot(density(par_out_reich[, 2], cut = c(0, 10000)), xlim = xlim, ylim = ylim, xlab  =  "annual respiration (gC m-2 yr-1)", ylab  =  "Arctic Deciduous",  main = "")
-points(density(par_out_atkin[, 2], cut = c(0, 10000)), type = "l", col = "blue")
-points(density(par_out_ryan[, 2], cut = c(0, 10000)), type  =  "l", col = "red")  
+plot(density(par_out_reich[, 2], cut = c(0, 10000)), xlim = xlim, ylim = ylim, xlab  =  "annual respiration (gC m-2 yr-1)", ylab  =  "Arctic Deciduous",  main = "", lty = "dotted")
+points(density(par_out_atkin[, 2], cut = c(0, 10000)), type = "l", col = "blue", lty = "dashed")
+points(density(par_out_ryan[, 2], cut = c(0, 10000)), type  =  "l", col = "red", lty = "solid")  
 mtext("density", side = 2, adj  =  0.6, line  =  2.5, cex = 0.7)
 mtext("Arctic Deciduous", side = 2, adj  =  0.6, line  =  4.5)
 mtext(xlab, side = 1, adj  =  0.6, line  =  2.5, cex = 0.7)
@@ -303,15 +303,16 @@ par(mfrow = c(3, 3), mar  =  c(1.1, 1.1, 1.1, 1.1), oma  =  c(5, 6, 2, 0))
 load("output/Rm_at_obs_LAI_TCN_biome3.Rdata")
 ylim  =  range(c(density(par_out_reich[, 2]/par_out_reich[, 1])$y, density(par_out_ryan[, 2]/par_out_ryan[, 1])$y), density(par_out_atkin[, 2]/par_out_atkin[, 1])$y)
 xlim  =  range(c(density(par_out_reich[, 2]/par_out_reich[, 1])$x, density(par_out_ryan[, 2]/par_out_ryan[, 1])$x), density(par_out_atkin[, 2]/par_out_atkin[, 1])$x)
-plot(density(par_out_reich[, 2]/par_out_reich[, 1]), xlim = xlim, ylim = ylim, main  =  "")
-points(density(par_out_atkin[, 2]/par_out_atkin[, 1]), type = "l", col = "blue")
-points(density(par_out_ryan[, 2]/par_out_ryan[, 1]), type  =  "l", col = "red")  
+plot(density(par_out_reich[, 2]/par_out_reich[, 1]), xlim = xlim, ylim = ylim, main  =  "", lty = "dotted")
+points(density(par_out_atkin[, 2]/par_out_atkin[, 1]), type = "l", col = "blue", lty = "dashed")
+points(density(par_out_ryan[, 2]/par_out_ryan[, 1]), type  =  "l", col = "red", lty = "solid")  
 v  =  expression(paste("Canopy ", R[leaf][",m"],"/GPP", sep = " "))
 mtext(v, side = 3, adj  =  0.6, line  =  1.0)
 text(xlim[1], ylim[2], "\n   (a)")
 mtext("density", side = 2, adj  =  0.6, line  =  2.5, cex = 0.7)
 mtext("Tropical Evergeen", side = 2, adj  =  0.6, line  =  4.5)
-legend("topright", c("Ryan 1991", "Atkin 2016", "Reich 2008"), lty = c(1, 1, 1), col = c("red", "blue", "black"), bty = "n")
+legend("topright", c("Ryan 1991", "Atkin 2016", "Reich 2008"), col = c("red", "blue", "black"), bty = "n", lty = c("solid", "dashed", "dotted"))
+
 
 #Blank
 plot.new()
@@ -320,9 +321,9 @@ plot.new()
 load("output/Rm_at_obs_LAI_TCN_biome2.Rdata")
 ylim  =  range(c(density(par_out_reich[, 2]/par_out_reich[, 1])$y, density(par_out_ryan[, 2]/par_out_ryan[, 1])$y), density(par_out_atkin[, 2]/par_out_atkin[, 1])$y)
 xlim  =  range(c(density(par_out_reich[, 2]/par_out_reich[, 1])$x, density(par_out_ryan[, 2]/par_out_ryan[, 1])$x), density(par_out_atkin[, 2]/par_out_atkin[, 1])$x)
-plot(density(par_out_reich[, 2]/par_out_reich[, 1]), xlim = xlim, ylim = ylim, xlab  =  "Rm/GPP Ratio",  main = "")
-points(density(par_out_atkin[, 2]/par_out_atkin[, 1]), type = "l", col = "blue")
-points(density(par_out_ryan[, 2]/par_out_ryan[, 1]), type  =  "l", col = "red")    
+plot(density(par_out_reich[, 2]/par_out_reich[, 1]), xlim = xlim, ylim = ylim, xlab  =  "Rm/GPP Ratio",  main = "", lty = "dotted")
+points(density(par_out_atkin[, 2]/par_out_atkin[, 1]), type = "l", col = "blue", lty = "dashed")
+points(density(par_out_ryan[, 2]/par_out_ryan[, 1]), type  =  "l", col = "red", lty = "solid")    
 mtext("density", side = 2, adj  =  0.6, line  =  2.5, cex = 0.7)
 mtext("Arctic Evergreen",  side = 2, adj  =  0.6, line  =  4.5)
 text(xlim[1],  ylim[2],  "\n   (b)")
@@ -333,9 +334,9 @@ plot.new()
 load("output/Rm_at_obs_LAI_TCN_biome1.Rdata")
 ylim = range(c(density(par_out_reich[, 2] / par_out_reich[,  1])$y, density(par_out_ryan[, 2] / par_out_ryan[, 1])$y), density(par_out_atkin[, 2] / par_out_atkin[, 1])$y)
 xlim = range(c(density(par_out_reich[, 2] / par_out_reich[, 1])$x, density(par_out_ryan[, 2] / par_out_ryan[, 1])$x), density(par_out_atkin[, 2] / par_out_atkin[, 1])$x)
-plot(density(par_out_reich[, 2] / par_out_reich[, 1]), xlim = xlim, ylim = ylim, xlab  =  "Rm/GPP Ratio", main = "")
-points(density(par_out_atkin[, 2] / par_out_atkin[, 1]), type = "l", col = "blue")
-points(density(par_out_ryan[, 2] / par_out_ryan[, 1]), type  =  "l", col = "red") 
+plot(density(par_out_reich[, 2] / par_out_reich[, 1]), xlim = xlim, ylim = ylim, xlab  =  "Rm/GPP Ratio", main = "", lty = "dotted")
+points(density(par_out_atkin[, 2] / par_out_atkin[, 1]), type = "l", col = "blue", lty = "dashed")
+points(density(par_out_ryan[, 2] / par_out_ryan[, 1]), type  =  "l", col = "red", lty = "solid") 
 text(xlim[1], ylim[2], "\n   (c)")
 mtext("density", side = 2, adj  =  0.6, line  =  2.5, cex = 0.7)
 mtext("Arctic Deciduous", side = 2, adj  =  0.6, line  =  4.5)
@@ -357,7 +358,7 @@ par(mfrow = c(3, 3), mar = c(1.1, 1.1, 1.1, 1.1), oma  =  c(5, 6, 2, 0))
 #########
 load("output/baseline_ryan_tropical_0.0106_1_contours.Rdata")
 contour(LAI, N, ((gpp - ra_mass) - leaf_growth_respiration - leaf_allocation), levels = seq(0, 7000, 200))
-points(leafC.linelist[[zero_iso_leafC]]$x, leafC.linelist[[zero_iso_leafC]]$y, type = "l", col = "red", lwd = 2, lty = "dashed")
+points(leafC.linelist[[zero_iso_leafC]]$x, leafC.linelist[[zero_iso_leafC]]$y, type = "l", col = "red", lwd = 2, lty = "dotted")
 points(leafN.linelist[[zero_iso_leafN]]$x, leafN.linelist[[zero_iso_leafN ]]$y, type = "l", col = "blue", lwd = 2, lty = "longdash")
 mtext(ylabel, side = 2, adj = 0.6, line  =  2.5, cex = 0.7)
 mtext("Tropical Evergeen", side = 2, adj  =  0.6, line  =  4.5)
@@ -368,7 +369,7 @@ abline(lm(obs_TFN ~ obs_LAI))
 #########
 load("output/baseline_atkin_tropical_1.756_0.2061_contours.Rdata")
 contour(LAI, N, ((gpp - ra_mass) - leaf_growth_respiration - leaf_allocation), levels = seq(0, 7000, 200))
-points(leafC.linelist[[zero_iso_leafC]]$x, leafC.linelist[[zero_iso_leafC]]$y, type = "l", col = "red", lwd = 2, lty = "dashed")
+points(leafC.linelist[[zero_iso_leafC]]$x, leafC.linelist[[zero_iso_leafC]]$y, type = "l", col = "red", lwd = 2, lty = "dotted")
 points(leafN.linelist[[zero_iso_leafN]]$x, leafN.linelist[[zero_iso_leafN ]]$y, type = "l", col = "blue", lwd = 2, lty = "longdash")
 points(obs_LAI, obs_TFN, pch = 20, cex = 2)
 mtext("Aktin et al. 2016", side = 3, adj  =  0.6, line  =  1.0)
@@ -377,7 +378,7 @@ abline(lm(obs_TFN ~ obs_LAI))
 #########
 load("output/baseline_reich_tropical_0.691_1.639_contours.Rdata")
 contour(LAI, N, ((gpp - ra_mass) - leaf_growth_respiration - leaf_allocation), levels = seq(0, 7000, 200))
-points(leafC.linelist[[zero_iso_leafC]]$x, leafC.linelist[[zero_iso_leafC]]$y, type = "l", col = "red", lwd = 2, lty = "dashed")
+points(leafC.linelist[[zero_iso_leafC]]$x, leafC.linelist[[zero_iso_leafC]]$y, type = "l", col = "red", lwd = 2, lty = "dotted")
 points(leafN.linelist[[zero_iso_leafN]]$x, leafN.linelist[[zero_iso_leafN ]]$y, type = "l", col = "blue", lwd = 2, lty = "longdash")
 points(obs_LAI, obs_TFN, pch = 20, cex = 2)
 mtext("Reich et al. 2008", side = 3, adj  =  0.6, line  =  1.0)
@@ -386,7 +387,7 @@ abline(lm(obs_TFN ~ obs_LAI))
 #########
 load("output/baseline_ryan_arctic_evergreen_0.0106_1_contours.Rdata")
 contour(LAI, N, ((gpp - ra_mass) - leaf_growth_respiration - leaf_allocation), levels = seq(0, 7000, 100), ylab  =  "Arctic Evergreen")
-points(leafC.linelist[[zero_iso_leafC]]$x, leafC.linelist[[zero_iso_leafC]]$y, type = "l", col = "red", lwd = 2, lty = "dashed")
+points(leafC.linelist[[zero_iso_leafC]]$x, leafC.linelist[[zero_iso_leafC]]$y, type = "l", col = "red", lwd = 2, lty = "dotted")
 points(leafN.linelist[[zero_iso_leafN]]$x, leafN.linelist[[zero_iso_leafN ]]$y, type = "l", col = "blue", lwd = 2, lty = "longdash")
 mtext(ylabel, side = 2, adj  =  0.6, line  =  2.5, cex = 0.7)
 mtext("Arctic Evergreen", side = 2, adj  =  0.6, line  =  4.5)
@@ -396,23 +397,23 @@ abline(lm(obs_TFN ~ obs_LAI))
 #########
 load("output/baseline_atkin_arctic_evergreen_1.756_0.2061_contours.Rdata")
 contour(LAI, N, ((gpp - ra_mass) - leaf_growth_respiration - leaf_allocation), levels = seq(0, 7000, 100))
-points(leafC.linelist[[zero_iso_leafC]]$x, leafC.linelist[[zero_iso_leafC]]$y, type = "l", col = "red", lwd = 2, lty = "dashed")
+points(leafC.linelist[[zero_iso_leafC]]$x, leafC.linelist[[zero_iso_leafC]]$y, type = "l", col = "red", lwd = 2, lty = "dotted")
 points(leafN.linelist[[zero_iso_leafN]]$x, leafN.linelist[[zero_iso_leafN ]]$y, type = "l", col = "blue", lwd = 2, lty = "longdash")
 text(0.4, 19, "(e)")
 points(obs_LAI, obs_TFN, pch = 20, cex = 2)
 abline(lm(obs_TFN ~ obs_LAI))
 #########
 load("output/baseline_reich_arctic_evergreen_0.691_1.639_contours.Rdata")
 contour(LAI, N, ((gpp - ra_mass) - leaf_growth_respiration - leaf_allocation), levels = seq(0, 7000, 100))
-points(leafC.linelist[[zero_iso_leafC]]$x, leafC.linelist[[zero_iso_leafC]]$y, type = "l", col = "red", lwd = 2, lty = "dashed")
+points(leafC.linelist[[zero_iso_leafC]]$x, leafC.linelist[[zero_iso_leafC]]$y, type = "l", col = "red", lwd = 2, lty = "dotted")
 points(leafN.linelist[[zero_iso_leafN]]$x, leafN.linelist[[zero_iso_leafN ]]$y, type = "l", col = "blue", lwd = 2, lty = "longdash")
 points(obs_LAI, obs_TFN, pch = 20, cex = 2)
 text(0.4, 19, "(f)")
 abline(lm(obs_TFN ~ obs_LAI))
 #########
 load("output/baseline_ryan_arctic_decid_0.0106_1_contours.Rdata")
 contour(LAI, N, ((gpp-ra_mass) - leaf_growth_respiration - leaf_allocation), levels = seq(0, 7000, 100),ylab  =  "Arctic Decidious")
-points(leafC.linelist[[zero_iso_leafC]]$x, leafC.linelist[[zero_iso_leafC]]$y, type = "l", col = "red", lwd = 2, lty = "dashed")
+points(leafC.linelist[[zero_iso_leafC]]$x, leafC.linelist[[zero_iso_leafC]]$y, type = "l", col = "red", lwd = 2, lty = "dotted")
 points(leafN.linelist[[zero_iso_leafN]]$x, leafN.linelist[[zero_iso_leafN ]]$y, type = "l", col = "blue", lwd = 2, lty = "longdash")
 mtext(ylabel, side = 2, adj  =  0.6, line  =  2.5, cex = 0.7)
 mtext("Arctic Deciduous", side = 2, adj  =  0.6, line  =  4.5)
@@ -423,7 +424,7 @@ abline(lm(obs_TFN ~ obs_LAI))
 #########
 load("output/baseline_atkin_arctic_decid_1.756_0.2061_contours.Rdata")
 contour(LAI, N, ((gpp-ra_mass) - leaf_growth_respiration - leaf_allocation), levels = seq(0, 7000, 100))
-points(leafC.linelist[[zero_iso_leafC]]$x, leafC.linelist[[zero_iso_leafC]]$y, type = "l", col = "red", lwd = 2, lty = "dashed")
+points(leafC.linelist[[zero_iso_leafC]]$x, leafC.linelist[[zero_iso_leafC]]$y, type = "l", col = "red", lwd = 2, lty = "dotted")
 points(leafN.linelist[[zero_iso_leafN]]$x, leafN.linelist[[zero_iso_leafN ]]$y, type = "l", col = "blue", lwd = 2, lty = "longdash")
 points(obs_LAI, obs_TFN, pch = 20, cex = 2)
 mtext(xlabel, side = 1, adj  =  0.6, line  =  2.5, cex = 0.7)
@@ -432,7 +433,7 @@ abline(lm(obs_TFN ~ obs_LAI))
 #########
 load("output/baseline_reich_arctic_decid_0.691_1.639_contours.Rdata")
 contour(LAI, N, ((gpp-ra_mass) - leaf_growth_respiration - leaf_allocation), levels = seq(0, 7000, 100))
-points(leafC.linelist[[zero_iso_leafC]]$x,leafC.linelist[[zero_iso_leafC]]$y, type = "l", col = "red", lwd = 2, lty = "dashed")
+points(leafC.linelist[[zero_iso_leafC]]$x,leafC.linelist[[zero_iso_leafC]]$y, type = "l", col = "red", lwd = 2, lty = "dotted")
 points(leafN.linelist[[zero_iso_leafN]]$x, leafN.linelist[[zero_iso_leafN ]]$y, type = "l", col = "blue", lwd = 2, lty = "longdash")
 points(obs_LAI, obs_TFN, pch = 20, cex = 2)
 mtext(xlabel, side = 1, adj  =  0.6, line  =  2.5, cex = 0.7)